buildGODatabaseDriver: buildGODatabaseDriver

In minimalistGODB: Build a Minimalist Gene Ontology (GO) Database (GODB)

buildGODatabaseDriver

Description

driver to build multiple GO databases for many species

Usage

buildGODatabaseDriver(goaDir, gobasic, dir = NULL, verbose = FALSE)

Arguments

goaDir	character string path name to directory containing downloaded goa .gaf files
gobasic	character string path name to downloaded go-basic.obo
dir	character string path name to directory to hold species database subdirectories
verbose	Boolean if TRUE print out some diagnostic info

Details

download goa .gaf files from https://current.geneontology.org/products/pages/downloads.html download go-basic.obo from https://geneontology.org/docs/download-ontology/

The output GOGOA3 was saved as an .RData file. This was too large for CRAN. It is available from https://github.com/barryzee/GO/tree/main/databases

Value

returns GO database with columns c("HGNC","GO","RELATION","NAME","ONTOLOGY")

Examples

## Not run: 
# replace my path names for goa and gobasic with your own!!
# these were obtained from the download sites listed in 'details' section
goaDir<-"/Users/barryzeeberg/Downloads/gaf/"
gobasic<-"~/go-basic.obo"
buildGODatabaseDriver(goaDir,gobasic,dir="~/personal",verbose=TRUE)

## End(Not run)

# here is a small example that you can run
goaDir<-system.file("extdata",package="minimalistGODB")
gobasic<-system.file("extdata","go-basic.small.obo",package="minimalistGODB")
dir<-tempdir()
buildGODatabaseDriver(goaDir,gobasic,dir,verbose=TRUE)

minimalistGODB documentation built on June 8, 2025, 11:41 a.m.